Modeling ionic liquids, diffusion on surfaces and catalysis: a graduate student looks high and low

A challenging area of computational chemistry is the accurate treatment of reactions taking place in solvents or on surfaces as in the fields of surface chemistry and heterogeneous catalysis. This thesis focuses on electronic structures studies of tetrazolium based ionic liquids, diffusion of Aluminium on the Si(100)-2x1 reconstructed surface, and the nitroaldol reaction. In addition a method for the interaction of the universal force field with the effective fragment potential method has been developed. Example calculations on small clusters of silica and water have been carrier out using this method

Molecular modelling aided design and synthesis of photochromic dyes containing a permanent chromophore

Photochromic dyes are a very important and relatively novel class of dyes. The usual, though not exclusive, behaviour of these dyes is to show a reversible colour change from colourless to coloured when exposed to UV light. Among the photochromic dye classes, spirooxazines and naphthopyrans were selected for investigation. An attempt was made to construct molecules with a permanent chromophore (azo) in spirooxazines as well as naphthopyrans separately, with a view to providing a colour change from one colour to another. Three different isomers of dihydroxynaphthalene were used as one group of starting materials for the synthesis of spirooxazines with the introduction of the azo (hydrazone) chromophore by coupling. Other starting materials used were anthraquinones, naphthoquinones and pyrazolones. A range of molecular modelling techniques (molecular mechanics, MM2 and quantum mechanics, AM1) using the CAChe system, were applied to predict optimized geometrical conformations and energies of the ring-closed form and ringopened merocyanine forms of all the dyes. PPP-MO calculations were also carried out to predict the potential colour of the dyes. The dyes were characterized using DSC, FTIR, NMR, UV-Visible spectroscopy and elemental analysis. The photochromic properties of one of the azospirooxazines was subjected to a detailed study under different experimental conditions, and showed a unique slow colour change from orange to grey.Worshipful Company of Dyers (London

Conformational dynamics and equilibria in amides

http://www.ester.ee/record=b1053476~S1*es

Challenges of and Insights into Acid-Catalyzed Transformations of Sugars

The selective transformation of hexose and pentose sugars to intermediate platform chemicals, such as furans, is an essential step in the conversion of cellulosic and hemicellulosic biomass to biofuels and biochemicals. Yet, many challenges in achieving commercially viable processes remain. In this feature article, we outline challenges that need to be overcome to enable these transformations. Then, we present the newly introduced acid-catalyzed isomerization of aldose sugars to ketose sugars via a class of solid Lewis acid catalysts (e.g., Sn-Beta, Ti-Beta). We elucidate mechanistic insights arising from subnanometer cooperativity and solvent effects that can be controlled to tune reaction pathways and selectivity and draw parallels between heterogeneous and homogeneous Lewis acid catalysts. Subsequently, we discuss fructose dehydration to 5-hydroxyl-methylfurfural (HMF) via homogeneous and heterogeneous Brønsted acid-catalyzed chemistry. We show how fundamental insights arising from the combination of kinetics, spectroscopy, and multiscale simulations rationalize the improved yield of HMF in water–organic cosolvents. The stability of heterogeneous Lewis acid catalysts under low pH enables tandem Brønsted and Lewis acid-catalyzed reactions in a single pot that overcomes equilibrium limitations and gives a high HMF yield starting from sugar raw materials. Additionally, we provide an overview of multicomponent adsorption of biomass derivatives from solution in microporous materials and discuss how structure–property relations can lead to superior micro- and micromesoporous carbon adsorbents for reactive adsorption toward high HMF yield. Finally, we provide an outlook for the field

Transannular effects in cage compounds : the alcohol-ketal exchange reaction of 3-methoxy-4-oxahexacyclo [5.4.1.0. 0?. 0?. 0?. ]? dodecane

The transannular effects in a homologous series of dimethoxy cage alochols were studied by use of physical methods such as infrared and nmr spectra. It was shown that a pronounced transannular effect occurred in these cage compounds which manifested itself as an increasingly stronger hydrogen bond between the hydroxyl proton and the endo-methoxyl oxygen as the number of carbon atoms increases in the C bridge. The occurrence of transannular effects in these compounds was also supported by an intramolecular alcohol-ketal exchange reaction and molecular mechanics calculations

Thermochemistry reaction paths and oxidation kinetics on ketonyl and aldehydic nitrogen oxides, propene and isooctane: a theoretical study

Thermochemical properties for several atmospheric and combustion related species are determined using computational chemical methods coupled with fundamentals of thermodynamics and statistical mechanics. Enthalpies of formation (ΔHf°298) are determined using isodesmic reaction analysis at the CBS-QB3 composite and the B3LYP density functional methods. Entropies (S°298) and heat capacities (Cp°(T)) are determined using geometric parameters and vibration frequencies; internal rotor contributions are included in S and Cp(T) values in place of torsion frequencies. Kinetic parameters are calculated versus pressure and temperature for the chemical activated formation and unimolecular dissociation. Multi-frequency quantum RRK (QRRK) analysis is used for k(E) with Master Equation analysis for fall off. Recommended values for enthalpies of formation of the most stable conformers of nitroacetone, acetonitrite, nitroacetate and acetyl nitrite are -51.6 kcal mol-1, -51.3 kcal mol-1, -45.4 kcal mol-1 and -58.2 kcal mol-1, respectively. The calculated ΔfH º298 for nitroethylene is 7.6 kcal mol-1 and for vinyl nitrite is 7.2 kcal mol-1. The chemically activated R• + NO2 systems associations proceed to RCO• + NO via chemical activation reaction with a fraction to stabilized adducts and lower energy products at atmospheric pressure and temperature. Thermochemical properties of isooctane (2,2,4-trimethyl pentane) and its four carbon radicals from loss of hydrogen atoms, and kinetics of the tertiary isooctane radical reaction with O2 are determined. The computed standard enthalpy of formation of isooctane from this study is -54.40 kcal mol-1. The major products from reaction of the tert-isooctane radical + O2 to form a chemically activated tert-isooctane-peroxy radical are formation of isooctene plus HO2. Next important products are cyclic ethers plus OH radical. This research is the first fundamentally based study of relevant pathways on the potential energy surfaces of tert-isooctane radicals + O2 using high level composite calculation methods. Kinetic modeling for OH addition to propene and subsequent O2 association to the hydroxyl-propyl radical adduct shows that significant forward reaction goes to regenerate OH radicals over the range of temperature and pressure studied. Recycle of OH from the decomposition of the hydroxyl propyl-peroxy radical is up to 78%. Inclusion of activation energy resulting from OH addition to primary carbon (double activation) does not show increase in OH recycle. The introduction of the rate constants presented in this study into existing reaction mechanisms should lead to better kinetic models for olefin oxidation chemistry the atmospheric

Orbital control and selectivity in addition reactions

Several topics which are relevant to the results and methods in this thesis are examined in Part I. Recent developments in the application of molecular orbital theory to the Diels-Alder reaction and the history and development of semi-empirical molecular orbital methods are reviewed. A survey of the major developments in understanding diastereofacial selection in the Diels-Alder reaction is also included in Part I. In Part II experimental and molecular mechanics studies are described for the addition of several azo, acetylenic and alkene dienophiles with four cage-fused dienes. Reactions of a dihydroxy substituted cage diene were found to proceed with complete selectivity for reaction from the face of the diene anti to the cyclobutane group, with the exception of the reaction of nitrosobenzene which was determined to be reversible. For most of the dienophiles, however, molecular mechanics calculations of the products in the reactions confirm that the relative stability of the adducts does not control the diastereofacial selection in the reaction. With a series of mono- and dimethylidene substituted cage-fused dienes, reactions of alkene dienophiles showed a strong preference for reaction from the anti face of the diene and this is successfully rationalized by a transition state model based on molecular mechanics. A series of mono and dimethylidene substituted cage dienes showed an opposing trend in facial selectivity, upon reaction with acetylenic dienophiles, to that observed with azo dienophiles. The selectivity observed for the reactions of acetylenic dienophiles cannot be rationalised by the "steric only" molecular mechanics based transition state models and this is interpreted as pointing to the importance of direct interactions between the substituents on the cage diene and the approaching dienophile. Several studies on the chemistry of cage-fused dienes are described with emphasis on the importance of transannular interaction during attempts to effect functional group interconversions of the cage substituents. Part III of this thesis reports studies using the AM1 and PM3 molecular orbital methods to examine several systems where orbital control may be important in determining facial selection. The reaction of acetylene with both simple dienes and cage-fused dienes is examined by application of the AM1 and PM3 methods. The reactions of acetylene with all the dienes studied are predicted to occur in reactions which are both concerted and synchronous. A detailed analysis of the energy changes in the molecular orbital energy levels during the reactions revealed destabilizing interactions involving the "orthogonal" HOMO of acetylenic dienophiles. These are important in determining the diastereofacial selection of reactions of acetylenic dienophiles with cage-fused dienes when there are suitably placed lone pairs on terminal substituents. The extent of σ/π interaction, determined by AM1 calculations for several cage-fused dienes, is shown to vary considerably with the nature of the cage substituents, but this is not considered to be an important factor in determining facial selection. As a model for substituted azo dienophiles, the Diels-Alder reactions of diimide (N₂H₂) have been studied by the PM3 method. This reaction is predicted to be both concerted and synchronous for the reaction of Z-diimide and butadiene in the exo mode but for the reaction of Z-diimide in the endo mode, the reaction is predicted to proceed via an unsymmetrical transition structure although still in a concerted reaction. The reaction of E-diimide with butadiene is considerably more complicated and three stationary points were located on the potential energy surface. The energy of aziridinium imide intermediates in possible two-step reactions of diimide and butadiene were evaluated by the PM3 method and determined to be approximately the same as the energy of the transition structures in the concerted reactions and so this precludes the involvement of these species in the reaction pathway. Finally the AM1 method was applied to examine the effect of substituents in determining the facial selection in the addition of methanol to 2,3- disubstituted-7-norbomanones and of ethylene to 5-substituted cyclopentadienes. Both of these systems have been proposed to show diastereofacial selection influenced by hyperconjugative stabilization. However, the AM1 method was not able to reproduce the observed facial selection in these reactions. The operation and function of several computer programs developed during the course work for the graphical analysis of the results of molecular mechanics and molecular orbital calculations and for quantifying σ/π interaction in dienes are described in the appendix

Thermochemistry of fluorinated aldehydes and corresponding radicals;thermochemistry and kinetics of diethyl ether and ethyl oxirane relative to reactions under atmospheric and combustion conditions

Fundamental thermochemical properties including enthalpies (ΔH°f 298), entropies (S°(T)), heat capacities (Cp(T)), and bond dissociation energies (BDEs) for several common and complex hydrocarbon fuel species are determined using computational chemical methods. ΔH°f 298 values are calculated using isodesmic reactions with the CBS-APNO, CBS-4M, CBS-QB3, G2, G3, G4, Weizmann-1 (W1U) and M06-2X, ωB97X, B3-LYP with basis set 6-31G+ (d,p) and 6-31G++(d,p) calculation methods. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated for contributions to entropies and heat capacities. Kinetic rate parameters are calculated for hydrogen abstraction and chemical activation reactions. The recommended ideal gas phase ΔH°f298 (kcal mole-1) values calculated for several normal hydrocarbons and fluorinated species including corresponding radicals from loss of hydrogen atoms show strong comparison to available literature values. Ethers C—H BDEs in the primary position in comparison to the secondary position increase by 3-8 kcal mole-1 for aliphatic chains. Cyclic ethers posses Entropies (S*298 in cal/mole K) are estimated using B3-LYP methodology with basis sets 6-31+G(d,p) and 6-31++G(d,p) computed frequencies and geometries. Rotational barriers are determined and hindered internal rotational contributions for S*298K and Cp(T) are calculated using the rigid rotor harmonic oscillator approximation, with direct integration over energy levels of intramolecular rotation potential energy curve. Thermochemical properties for the fluorinated carbon groups CO/C/F, C/CO/F3, C/CO/F/H2, C/C/CO/F/H, C/C/CO/F2, and C/C/CO/F/H are investigated. Previously published enthalpies for fluoroacetaldehyde, fluoroacetaldehyde fluoride, difluoroacetaldehyde, difluoroacetaldehyde fluoride, trifluoroacetaldehyde and trifluoroacetaldehyde fluoride that were previously determined via isodesmic reactions schemes are revised using updated reference species values